When using TWAIN, the printer makes no decision on filetype or structure, the application that is using TWAIN does that. So if you don't have a pdf option, it is the applications fault. Windows Fax and Scan as well as the new Win 10 one just called Scan both don't give pdf as an option.
Windows Picture viewer doesn't support mTIFF (multipage tiff) so you would need it in file per page format.
For mTIFF I suggest Irfanview
There are a plethora of free apps that do pdf, my suggestion (Mine, not Xerox's) would be NAPS2 because of the large community that helps support it, and it has a pretty robust feature set.
I work for Xerox, I have no relation to either application I list and don't support them in any way. I have never used Page Manager or even heard of it so I have no comment's on how it works.